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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ), 'gf_id' => 'HOM05D001260', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001260' ), 'data_identifier' => 'HOM05D001260', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001260', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '496', 'num_species' => '100' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p42030' => 'bna', 'A03p02490' => 'bna', 'A05p38010' => 'bna', 'A09p48630' => 'bna', 'A10p30380' => 'bna', 'Aa31LG10G10650' => 'aar', 'Aa31LG11G7010' => 'aar', 'Aa31LG11G7020' => 'aar', 'Aa31LG3G2700' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1235' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.891' => 'aag', 'Actinidia02910' => 'ach', 'Actinidia02911' => 'ach', 'Actinidia17679' => 'ach', 'Actinidia38144' => 'ach', 'Ah.10g037130' => 'amhyb', 'Ah.13g074360' => 'amhyb', 'Ah.13g076750' => 'amhyb', 'Ah.13g076760' => 'amhyb', 'AL3G21490' => 'aly', 'AL3G22890' => 'aly', 'AL5G36840' => 'aly', 'AL6G15910' => 'aly', 'AL6G15920' => 'aly', 'Aqoxy1G00447' => 'aox', 'Aqoxy1G00821' => 'aox', 'arahy.Tifrunner.gnm1.ann1.1DVI41' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1G1YD8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU85I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TM7LMJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.YN8NC1' => 'arhy', 'AT3G10160' => 'ath', 'AT3G55630' => 'ath', 'AT5G05970' => 'ath', 'AT5G05980' => 'ath', 'ATR0559G016' => 'atr', 'ATR0559G059' => 'atr', 'ATR0721G042' => 'atr', 'Atru.chr1.1242' => 'acertr', 'Atru.chr1.1243' => 'acertr', 'Atru.chr12.293' => 'acertr', 'Atru.chr12.295' => 'acertr', 'Atru.chr12.297' => 'acertr', 'Atru.chr12.334' => 'acertr', 'Atru.chr12.335' => 'acertr', 'AUR62002609' => 'cqu', 'AUR62012149' => 'cqu', 'AUR62026132' => 'cqu', 'AUR62030032' => 'cqu', 'AUR62030397' => 'cqu', 'AUR62034960' => 'cqu', 'AUR62040687' => 'cqu', 'AUR62041248' => 'cqu', 'BcaB01g00073' => 'bca', 'BcaB01g05749' => 'bca', 'BcaB01g05967' => 'bca', 'BcaB04g21228' => 'bca', 'BcaB05g21687' => 'bca', 'BcaB06g25631' => 'bca', 'BcaB08g35339' => 'bca', 'BcaC06g32308' => 'bca', 'BcaC06g32312' => 'bca', 'BcaC07g39893' => 'bca', 'BcaC09g48114' => 'bca', 'BcaNung06227' => 'bca', 'BcaNung06229' => 'bca', 'BcaNung07355' => 'bca', 'BolC1t05419H' => 'bol', 'BolC2t06221H' => 'bol', 'BolC3t12838H' => 'bol', 'BolC5t34341H' => 'bol', 'BolC8t50720H' => 'bol', 'BolC9t59840H' => 'bol', 'BolC9t59841H' => 'bol', 'BraA01t04271Z' => 'bra', 'BraA03t09610Z' => 'bra', 'BraA05t22592Z' => 'bra', 'BraA09t40315Z' => 'bra', 'BraA10t45076Z' => 'bra', 'BraA10t45077Z' => 'bra', 'C02p02540' => 'bna', 'C02p30030' => 'bna', 'C03p02830' => 'bna', 'C05p56770' => 'bna', 'C08p30970' => 'bna', 'C09p70820' => 'bna', 'CAN.G115.2' => 'can', 'CAN.G1237.17' => 'can', 'CAN.G505.16' => 'can', 'CAN.G945.9' => 'can', 'CAN.G986.45' => 'can', 'CAN.G986.46' => 'can', 'CANSAT56G0693' => 'cansat', 'CANSAT56G4350' => 'cansat', 'CANSAT80G1783' => 'cansat', 'CARHR084640' => 'chi', 'CARHR085910' => 'chi', 'CARHR129010' => 'chi', 'CARHR165690' => 'chi', 'CARHR207230' => 'chi', 'CARHR207240' => 'chi', 'Carub.0003s0931' => 'cru', 'Carub.0005s2238' => 'cru', 'Carub.0006s0486' => 'cru', 'Carub.0006s0487' => 'cru', 'Ca_05847_v3' => 'car', 'Ca_07493_v3' => 'car', 'Ca_11914_v3' => 'car', 'Ca_14429_v3' => 'car', 'Ca_16501_v3' => 'car', 'Ca_17117_v3' => 'car', 'Ca_17120_v3' => 'car', 'Ca_30976_v3' => 'car', 'CBR_g18739' => 'cbr', 'CBR_g37200' => 'cbr', 'Cc02_g07290' => 'ccan', 'Cc02_g07310' => 'ccan', 'Cc06_g18390' => 'ccan', 'CDE01G0546' => 'cde', 'CDE02G1800' => 'cde', 'CDE04G0745' => 'cde', 'CDE04G1242' => 'cde', 'CDE04G3718' => 'cde', 'Cfa016751' => 'cfa', 'Cfa026813' => 'cfa', 'Ciclev10004610m.g' => 'ccl', 'Ciclev10030832m.g' => 'ccl', 'Ciclev10031375m.g' => 'ccl', 'Ciclev10033371m.g' => 'ccl', 'Ciclev10033559m.g' => 'ccl', 'Ciclev10033785m.g' => 'ccl', 'CiPaw.01G292400' => 'cil', 'CiPaw.02G187400' => 'cil', 'CiPaw.09G042500' => 'cil', 'CiPaw.10G036800' => 'cil', 'ClCG09G018830' => 'cla', 'ClCG10G015570' => 'cla', 'ClCG11G006570' => 'cla', 'COL.COLO4_25528' => 'col', 'COL.COLO4_25532' => 'col', 'COL.COLO4_36753' => 'col', 'Cpa.g.sc120.13' => 'cpa', 'Cpa.g.sc19.263' => 'cpa', 'Cpa.g.sc776.1' => 'cpa', 'Cre05.g239067' => 'cre', 'Cre05.g239100' => 'cre', 'Cre13.g565150' => 'cre', 'CsaV3_3G040860' => 'csa', 'CsaV3_5G037300' => 'csa', 'CsaV3_6G001430' => 'csa', 'CSS0005230' => 'camsi', 'CSS0028733' => 'camsi', 'CSS0048341' => 'camsi', 'CSS0050084' => 'camsi', 'DCAR_011747' => 'dca', 'DCAR_020536' => 'dca', 'DCAR_024867' => 'dca', 'Dinv16265' => 'din', 'Dinv16267' => 'din', 'Dinv30294' => 'din', 'Dinv34465' => 'din', 'Dinv34467' => 'din', 'Duzib114G0737' => 'dzi', 'Duzib114G0845' => 'dzi', 'Duzib128G0118' => 'dzi', 'ECA232G0943' => 'eca', 'ECA233G1462' => 'eca', 'ECA233G4014' => 'eca', 'EL10Ac2g04684' => 'bvu', 'EL10Ac3g06309' => 'bvu', 'EL10Ac3g07165' => 'bvu', 'Eucgr.A02294' => 'egr', 'Eucgr.J02122' => 'egr', 'Eucgr.J02123' => 'egr', 'FAN01G0513' => 'fan', 'FAN01G0960' => 'fan', 'FAN02G0718' => 'fan', 'FAN02G3099' => 'fan', 'FAN03G2667' => 'fan', 'FAN03G3127' => 'fan', 'FAN03G3497' => 'fan', 'FAN04G1727' => 'fan', 'FAN05G2308' => 'fan', 'FAN06G1256' => 'fan', 'FAN06G1330' => 'fan', 'FAN06G3528' => 'fan', 'FAN06G4376' => 'fan', 'FAN10G0370' => 'fan', 'FAN14G5289' => 'fan', 'FAN18G2887' => 'fan', 'FvH4_6g24860' => 'fve', 'FvH4_7g23490' => 'fve', 'FvH4_7g23510' => 'fve', 'FvH4_7g23851' => 'fve', 'Glyma.02G191500' => 'gma', 'Glyma.02G251400' => 'gma', 'Glyma.02G251500' => 'gma', 'Glyma.10G105400' => 'gma', 'Glyma.14G065300' => 'gma', 'Glyma.14G065400' => 'gma', 'Glyma.18G034200' => 'gma', 'Gohir.A05G302400' => 'ghi', 'Gohir.A06G165900' => 'ghi', 'Gohir.A10G224000' => 'ghi', 'Gohir.D05G301900' => 'ghi', 'Gohir.D06G171200' => 'ghi', 'Gohir.D06G171300' => 'ghi', 'Gohir.D10G236300' => 'ghi', 'Gohir.D10G236616' => 'ghi', 'Gohir.D10G236624' => 'ghi', 'Gohir.D10G237000' => 'ghi', 'Gorai.009G320000' => 'gra', 'Gorai.011G270200' => 'gra', 'Gorai.011G270300' => 'gra', 'Gorai.011G270500' => 'gra', 'Gorai.011G270600' => 'gra', 'Gorai.011G270700' => 'gra', 'GSVIVG01008874001' => 'vvi', 'GSVIVG01016463001' => 'vvi', 'GSVIVG01016464001' => 'vvi', 'GSVIVG01033555001' => 'vvi', 'GSVIVG01038496001' => 'vvi', 'HanXRQChr02g0039031' => 'han', 'HanXRQChr08g0221221' => 'han', 'HanXRQChr08g0221231' => 'han', 'HanXRQChr09g0247031' => 'han', 'HanXRQChr10g0298631' => 'han', 'Haze_17131' => 'cav', 'Haze_17132' => 'cav', 'Haze_19753' => 'cav', 'Haze_26977' => 'cav', 'Hma1.2p1_0026F.1_g016500' => 'hma', 'Hma1.2p1_0039F.1_g024730' => 'hma', 'Hma1.2p1_0039F.1_g024740' => 'hma', 'Hma1.2p1_0056F.1_g031650' => 'hma', 'Hma1.2p1_0222F.1_g093450' => 'hma', 'Hma1.2p1_0222F.1_g093470' => 'hma', 'HPP92_006713' => 'vpl', 'HPP92_018157' => 'vpl', 'HPP92_018172' => 'vpl', 'HPP92_020546' => 'vpl', 'HPP92_020547' => 'vpl', 'HPP92_020548' => 'vpl', 'Hund12217' => 'sun', 'Hund12219' => 'sun', 'Hund16049' => 'sun', 'Hund19123' => 'sun', 'Hund22801' => 'sun', 'Hund24657' => 'sun', 'Lalb_Chr04g0250961' => 'lal', 'Lalb_Chr04g0250971' => 'lal', 'Lalb_Chr10g0104791' => 'lal', 'Lalb_Chr15g0084491' => 'lal', 'Lalb_Chr17g0346411' => 'lal', 'Lj5g0016803' => 'lja', 'Lj6g0027495' => 'lja', 'Lj8A76T111' => 'lonja', 'Lj8C77T9' => 'lonja', 'LjContig00141g0013846' => 'lja', 'LjContig00141g0022758' => 'lja', 'Lsat_1_v5_gn_2_60481' => 'lsa', 'Lsat_1_v5_gn_8_126841' => 'lsa', 'Lsat_1_v5_gn_8_14640' => 'lsa', 'Lsat_1_v5_gn_8_14661' => 'lsa', 'Lsat_1_v5_gn_9_31960' => 'lsa', 'Lsat_1_v5_gn_9_63441' => 'lsa', 'Manes.07G121400' => 'mes', 'Manes.08G053400' => 'mes', 'Manes.09G016200' => 'mes', 'Manes.10G022400' => 'mes', 'Manes.10G022675' => 'mes', 'Manes.10G022900' => 'mes', 'Manes.10G023400' => 'mes', 'Mapoly0010s0086' => 'mpo', 'Mapoly0118s0019' => 'mpo', 'MBI04_g44160_MAGBIO' => 'mbi', 'MBI05_g02647_MAGBIO' => 'mbi', 'MBI05_g44758_MAGBIO' => 'mbi', 'MBI08_g43731_MAGBIO' => 'mbi', 'MBI14_g06400_MAGBIO' => 'mbi', 'MBI15_g47610_MAGBIO' => 'mbi', 'MBI16_g06311_MAGBIO' => 'mbi', 'MBI18_g33591_MAGBIO' => 'mbi', 'MCO03G102' => 'mco', 'MCO10G081' => 'mco', 'MD01G1140600' => 'mdo', 'MD01G1140700' => 'mdo', 'MD07G1204900' => 'mdo', 'MD07G1205000' => 'mdo', 'MD14G1081100' => 'mdo', 'Medtr1g051385' => 'mtr', 'Medtr3g069160' => 'mtr', 'Medtr3g069180' => 'mtr', 'Medtr5g081240' => 'mtr', 'Medtr5g081250' => 'mtr', 'MELO3C008247.2' => 'cme', 'MELO3C009821.2' => 'cme', 'MELO3C021530.2' => 'cme', 'Migut.F00740' => 'egut', 'Migut.F01300' => 'egut', 'Migut.J01699' => 'egut', 'MSTRG.259' => 'ama', 'MSTRG.6400' => 'ama', 'Nitab4.5_0000647g0200' => 'nta', 'Nitab4.5_0000779g0070' => 'nta', 'Nitab4.5_0000826g0240' => 'nta', 'Nitab4.5_0001618g0320' => 'nta', 'Nitab4.5_0004474g0060' => 'nta', 'Nitab4.5_0006999g0050' => 'nta', 'Nn2g11262' => 'nnu', 'Nn2g13504' => 'nnu', 'Nn2g15056' => 'nnu', 'Oeu001521.1' => 'oeu', 'Oeu006928.1' => 'oeu', 'Oeu031370.1' => 'oeu', 'Oeu039009.1' => 'oeu', 'Os03g0111100' => 'osa', 'Os09g0267500' => 'osa', 'Os10g0503200' => 'osa', 'Peaxi162Scf00130g01018' => 'pax', 'Peaxi162Scf00164g01517' => 'pax', 'Peaxi162Scf00611g00324' => 'pax', 'Peaxi162Scf01064g00257' => 'pax', 'PGR004G2299' => 'pgr', 'PGR044G0660' => 'pgr', 'PGR044G1255' => 'pgr', 'PGSC0003DMG400021693' => 'stu', 'PGSC0003DMG400027193' => 'stu', 'Phvul.007G249200' => 'pvu', 'Phvul.008G230000' => 'pvu', 'Phvul.008G230100' => 'pvu', 'Potri.006G045400' => 'ptr', 'Potri.008G060600' => 'ptr', 'Potri.008G060700' => 'ptr', 'Potri.010G197700' => 'ptr', 'Potri.010G197800' => 'ptr', 'Potri.016G041800' => 'ptr', 'Pp3c13_5000' => 'ppa', 'Pp3c23_670' => 'ppa', 'Pp3c24_9100' => 'ppa', 'Pp3c26_11450' => 'ppa', 'Pp3c3_3110' => 'ppa', 'Pp3c4_30600' => 'ppa', 'PRCOL_00006377' => 'pco', 'Prupe.2G241100' => 'ppe', 'Prupe.2G241200' => 'ppe', 'Prupe.7G049800' => 'ppe', 'Psat0s3732g0200' => 'psa', 'Psat2g006760' => 'psa', 'Psat2g096440' => 'psa', 'Psat2g096560' => 'psa', 'Psat5g128680' => 'psa', 'Psat6g118120' => 'psa', 'Psat7g258800' => 'psa', 'Psat7g258880' => 'psa', 'PSO339G0232' => 'pso', 'PSO339G2799' => 'pso', 'PSO339G3002' => 'pso', 'PSO384G2321' => 'pso', 'PSO384G2594' => 'pso', 'PSO384G2968' => 'pso', 'PSO541G1624' => 'pso', 'PSO675G4234' => 'pso', 'QL07p004945' => 'qlo', 'QL07p004976' => 'qlo', 'QL08p061707' => 'qlo', 'QL08p061736' => 'qlo', 'QL08p061745' => 'qlo', 'RcHm_v2.0_Chr1g0315431' => 'rch', 'RcHm_v2.0_Chr1g0324411' => 'rch', 'RcHm_v2.0_Chr1g0368621' => 'rch', 'RcHm_v2.0_Chr1g0368661' => 'rch', 'RcHm_v2.0_Chr1g0369591' => 'rch', 'RcHm_v2.0_Chr2g0097681' => 'rch', 'RcHm_v2.0_Chr3g0484551' => 'rch', 'RcHm_v2.0_Chr4g0410221' => 'rch', 'RcHm_v2.0_Chr4g0410231' => 'rch', 'RcHm_v2.0_Chr4g0410241' => 'rch', 'RcHm_v2.0_Chr6g0278311' => 'rch', 'Rhsim03G0136800' => 'rsi', 'Rhsim03G0137000' => 'rsi', 'Rhsim04G0027700' => 'rsi', 'Rhsim04G0034300' => 'rsi', 'Rhsim04G0108100' => 'rsi', 'Rhsim06G0126400' => 'rsi', 'Rhsim08G0019500' => 'rsi', 'Rhsim08G0019600' => 'rsi', 'Rhsim08G0025600' => 'rsi', 'Rhsim09G0169300' => 'rsi', 'Sabra06G0031100' => 'sbr', 'Sabra08G0044700' => 'sbr', 'Sabra08G0044800' => 'sbr', 'Sabra10G0152100' => 'sbr', 'Sabra10G0152200' => 'sbr', 'Sabra10G0152300' => 'sbr', 'Sabra16G0047500' => 'sbr', 'SalBow6G0138' => 'sbo', 'SalBow6G0774' => 'sbo', 'SalBow6G0807' => 'sbo', 'SalBow6G1429' => 'sbo', 'SalBow6G3532' => 'sbo', 'Sc05g0005760' => 'sci', 'Sc10g0001890' => 'sci', 'Sc25g0005380' => 'sci', 'Sed0000163' => 'sed', 'Sed0004245' => 'sed', 'Sed0007578' => 'sed', 'Sed0025441' => 'sed', 'Sed0025459' => 'sed', 'SEGI_02085' => 'sgi', 'SEGI_03942' => 'sgi', 'SEGI_05272' => 'sgi', 'SEGI_21448' => 'sgi', 'SEGI_23725' => 'sgi', 'SEGI_35518' => 'sgi', 'SEGI_37873' => 'sgi', 'SGA_v2.0_scaffold105G30347' => 'sas', 'SGA_v2.0_scaffold108G31006' => 'sas', 'SGA_v2.0_scaffold221G42704' => 'sas', 'SGA_v2.0_scaffold2G00988' => 'sas', 'SGA_v2.0_scaffold2G01050' => 'sas', 'SGA_v2.0_scaffold318G48508' => 'sas', 'SHI03642' => 'shi', 'SHI03643' => 'shi', 'SHI03646' => 'shi', 'SHI03647' => 'shi', 'SMO140G0015' => 'smo', 'SMO169G0008' => 'smo', 'SMO222G0007' => 'smo', 'SMO230G0070' => 'smo', 'SMO271G0180' => 'smo', 'SMO367G0088' => 'smo', 'SMO367G0248' => 'smo', 'Solyc03g079920.3' => 'sly', 'Solyc04g016550.4' => 'sly', 'Solyc04g016560.2' => 'sly', 'Solyc05g052920.4' => 'sly', 'Sopen03g027210' => 'spe', 'Sopen04g008630' => 'spe', 'Sopen05g031430' => 'spe', 'Sp3g08440' => 'spa', 'Sp3g09610' => 'spa', 'Sp5g06840' => 'spa', 'Sp6g36910' => 'spa', 'Sp6g36920' => 'spa', 'TAR369G0466' => 'tar', 'TAR633G1227' => 'tar', 'TAR636G1361' => 'tar', 'TAR636G1929' => 'tar', 'TAR636G2673' => 'tar', 'THA.LOC104816401' => 'tha', 'THA.LOC104816577' => 'tha', 'THA.LOC104824300' => 'tha', 'THA.LOC104826868' => 'tha', 'Thecc.05G144800' => 'tca', 'Thecc.10G033200' => 'tca', 'Thecc.10G033600' => 'tca', 'Thecc.10G034300' => 'tca', 'Thhalv10010319m.g' => 'esa', 'Thhalv10012734m.g' => 'esa', 'Thhalv10013069m.g' => 'esa', 'Thhalv10020101m.g' => 'esa', 'Thhalv10020301m.g' => 'esa', 'TPR.G10326' => 'tpr', 'TPR.G1704' => 'tpr', 'TPR.G19653' => 'tpr', 'TPR.G25828' => 'tpr', 'TPR.G25838' => 'tpr', 'TPR.G25852' => 'tpr', 'TPR.G29632' => 'tpr', 'TPR.G35592' => 'tpr', 'TPR.G40812' => 'tpr', 'TWI38G0285' => 'twi', 'TWI38G0361' => 'twi', 'TWI53G1708' => 'twi', 'TWI63G0278' => 'twi', 'TWI63G0421' => 'twi', 'unitig_27.g25070' => 'ugi', 'unitig_37.g12012' => 'ugi', 'unitig_37.g12703' => 'ugi', 'unitig_744.g24617' => 'ugi', 'unitig_744.g24618' => 'ugi', 'vmacro07027' => 'vma', 'vmacro07029' => 'vma', 'vmacro09042' => 'vma', 'vmacro10208' => 'vma', 'vmacro10209' => 'vma', 'VMungo0647G0039' => 'vmu', 'VMungo0647G2094' => 'vmu', 'VMungo0720G2943' => 'vmu', 'Zm00001eb044170' => 'zma', 'Zm00001eb095480' => 'zma', 'Zm00001eb299330' => 'zma', 'Zm00001eb358850' => 'zma', 'Zm00001eb404110' => 'zma', 'Zm00001eb421680' => 'zma' ) $gf_id = 'HOM05D001260' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001260' ) $data_identifier = 'HOM05D001260' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 11, 'aar' => (int) 4, 'aag' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 4, 'aly' => (int) 5, 'aox' => (int) 2, 'arhy' => (int) 5, 'ath' => (int) 4, 'atr' => (int) 3, 'acertr' => (int) 7, 'cqu' => (int) 8, 'bca' => (int) 14, 'bol' => (int) 7, 'bra' => (int) 6, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 6, 'cru' => (int) 4, 'car' => (int) 8, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 5, 'cfa' => (int) 2, 'ccl' => (int) 6, 'cil' => (int) 4, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 3, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 3, 'eca' => (int) 3, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 16, 'fve' => (int) 4, 'gma' => (int) 7, 'ghi' => (int) 10, 'gra' => (int) 6, 'vvi' => (int) 5, 'han' => (int) 5, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 6, 'sun' => (int) 6, 'lal' => (int) 5, 'lja' => (int) 4, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 8, 'mco' => (int) 2, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 3, 'ama' => (int) 2, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 4, 'osa' => (int) 3, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 6, 'ppa' => (int) 6, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 8, 'pso' => (int) 8, 'qlo' => (int) 5, 'rch' => (int) 11, 'rsi' => (int) 10, 'sbr' => (int) 7, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 6, 'shi' => (int) 4, 'smo' => (int) 7, 'sly' => (int) 4, 'spe' => (int) 3, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 4, 'tca' => (int) 4, 'esa' => (int) 5, 'tpr' => (int) 9, 'twi' => (int) 5, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 3, 'zma' => (int) 6 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb421680' $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